Pinned Repositories
ArgoWorkflowGenerator
Java based workflow generator to deploy WES variant detection pipelines on Kubernetes using Argo. Reads WDL files and produces Argo compatible work flows specifciying compute cluster environment (pod) on which the workflow component should be executed and the buckets in which the results should be dropped
backpropagationneuralnetwork
backTranslationProteinToPutativeDNA
Gives most probable and least probable DNA Sequences for input protein sequence
BaselineSurveyResponseSimulator
Simulation of baseline survey response variables to store information in EPIC Number of variables: 495 Code: Java 8 Reads in csv file of variables and value range of permitted responses Use randomization to a) induce error b) generate valid responses, and simulate 1M responses, to use as prototype data to populate i2b2 deployments in support of the MVP project for VABHS
caBIO-load-scripts
ETL scripts to populate caBIO database
calculateCodonFrequency
perl script that reads file in multifasta format and complements it
caMODloadscripts
ETL scripts to populate caMOD database with MTB data from Jackson Labs
fastqcparser
Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, per tile sequence quality
GeneAbundance
rebase-using-kmp
restriction enzyme cleavage site identifier using kmp algorithm and REBASE
lvn3668's Repositories
lvn3668/ArgoWorkflowGenerator
Java based workflow generator to deploy WES variant detection pipelines on Kubernetes using Argo. Reads WDL files and produces Argo compatible work flows specifciying compute cluster environment (pod) on which the workflow component should be executed and the buckets in which the results should be dropped
lvn3668/backTranslationProteinToPutativeDNA
Gives most probable and least probable DNA Sequences for input protein sequence
lvn3668/calculateCodonFrequency
perl script that reads file in multifasta format and complements it
lvn3668/elegant-scipy
1st Edition of Elegant SciPy (O'Reilly Publishers)
lvn3668/FreezerworksInterfaceModule
Interface to Biomek that performs 1D and 2D Scan of aliquots (2d) and rack (1d) ; reads freezer configuration from DB and assigns location to plate
lvn3668/paralogIdentification
Wrapper script that calls formatdb on nr database and then runs blastall against formatted db and parses the output.